greyhole --fsck --find-orphaned-files --dir=/var/hda/files/drives/bay2/gh

This will run an fsck on the drive mounted in /var/hda/files/drives/bay2 and look for files without metadata. <br />

Repeat this for each drive you have changed the mount points for.<br />

At this point, your files should begin reappearing in your shares. If not, try running another fsck:

greyhole --fix-symlinks

greyhole --fsck